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Military bases in Iraq and Afghanistan continue to use waste methods that expose troops to potentially toxic emissions without fully understanding the effects, according to a new government audit obtained by CNN.

Between September 2009 and October 2010, investigators from the Government Accountability Office visited four bases in Iraq and reviewed planning documents on waste disposal for bases in Afghanistan. None of the Iraq bases visited were in compliance with military regulations. All four burned plastic -- which generates harmful emissions -- despite regulations against doing so.

The emissions have been the source of controversy as troops have complained about a host of problems, from cancerous tumors to respiratory issues, blaming exposure to burn pits. Military officials have denied any consequential effects on most troops.

The military, the report concluded, has been slow in using alternatives and has not considered the long-term costs of dealing with subsequent health issues.

Prior to an initial outcry about the pits more two years ago, the largest base in Iraq -- Balad Air Base -- was burning everything from hazardous and medical waste to plastics, using jet fuel as accelerant, according to military documents. The smoke poured over the living quarters and the base hospital, exposing thousands of troops to the emissions.

GAO investigators blame the continued burning of prohibited items on the constraints of operating in a war zone, limitations of resources and outdated agreements with waste disposal contractors that do not include the latest regulations on what is safe to burn.

The U.S. military generates about 10 pounds of non-hazardous waste per service member each day and "may consist of plastic, Styrofoam, and food from dining facilities; discarded electronics; shipping materials such as wooden pallets and plastic wrap; appliances; and other items such as mattresses, clothing, tires, metal containers, and furniture," the report says.

According to the report, there were 221 burn pits in Afghanistan by August and more are anticipated. Only 21 remained in Iraq and, like the troop levels there, the numbers are expected to decrease. The burn pits are operated by either the military or contractors.

While the pits have been in use since the beginning of each war, regulations and guidance were only issued in 2009 -- eight years into the Afghanistan conflict and six years after the start of the war in Iraq.

Incinerators and recycling would make for a much safer environment, but to date there are only 20 incinerators in Afghanistan and 41 in Iraq. Military officials complained they "were expensive and posed acquisition, logistic, and operational challenges," according to the report. However, the GAO found that the Department of Defense has little understanding of that cost.

"Our analysis determined that DOD has little information on what it costs to procure, install, operate, and maintain incinerators during contingency operations," said the report.

Additionally, the GAO found that sorting of trash and recycling efforts are only beginning in Iraq and have not been planned for in Afghanistan.

The report notes that the 2009 directive for Afghanistan regarding waste said while burning trash at the beginning of military operations is understandable, "open burning will not be the regular method of solid waste disposal."

A March 2010 military directive allows for burning waste only if the commander determines there is no other feasible method of waste disposal and petitions the Pentagon to do so. GAO investigators noted that as of August 2010, no commander had requested such permission. However, a senior military official told investigators that "information gathered from field commanders led him to conclude that disposal of prohibited items in burn pits had become routine at many bases in Afghanistan and Iraq."

The military's attitude about the impact of the burn pits has shifted. When complaints initially arose in 2008 military officials denied there was any hazard to troops. Last year the Pentagon changed that position, declaring long-term effects for troops who had pre-existing conditions was foreseeable.

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